On Tue, Feb 6, 2018 at 10:42 AM, Alexis Parenty <
alexis.parenty.h...@gmail.com> wrote:

>  I will try your approach and will nest all the result smiles  into a
> unique recursive smiles.
>
I'm not quite sure what you mean here, but it sounds unlikely to work. I
think you may need to do a SMILES for each of your isosteres.
After hitting "reply" on the earlier message I realized that this is a nice
example for a blog post, so I am going to put together some example code
that you may find useful.
I would be happy to do the example with your isosteres, but I need some
kind of explanation of what the actual substitution patterns are. For
example, you have these three "duplicates" in your original message;
'C1=CN=[CH1][CH1]=N1', 'C1=[CH1]N=C[CH1]=N1', 'C1=[CH1]N=[CH1]C=N1'
Should I interpret these as:
*C1=C(*)N=CC=N1
*C1=CN=C(*)C=N1
*C1=CN=CC(*) =N1
?

If that's right, does direction matter? If I apply the second of those
possibilities - *C1=CN=C(*)C=N1 - to
ClC(=O)NBr
should it yield both:
ClC1=CN=C (Br)C=N1
and
BrC1=CN=C(Cl)C=N1
or just one of them?


Best,
-greg





On 6 February 2018 at 07:54, Greg Landrum <greg.land...@gmail.com> wrote:
>
>> Hi Alexis,
>>
>> If you have substructures with substitutions at a single atom, it tends
>> to be simpler to use Chem.ReplaceSubstructs to do this. This is, however,
>> not the case here (or in general for bioisosteric replacement)
>>
>> The most flexible way to do what you're looking for is to use the RDKit's
>> chemical reaction functionality and create one reaction per isosteric
>> replacement you want to make. Here's a simple example showing the "amide ->
>> 1,2,3 triazole" replacement:
>>
>> In [11]: triazoleRxn = AllChem.ReactionFromSmarts('[*
>> :1]C(=O)N[*:2]>>[*:1]c1cn([*:2])nn1')
>>
>>
>> And here's how you'd use that to perform a replacement:
>>
>> In [12]: ps = triazoleRxn.RunReactants((Chem
>> .MolFromSmiles('C1CC1C(=O)Nc1ccccc1'),))
>>
>> In [13]: Chem.MolToSmiles(ps[0][0])
>> Out[13]: 'c1ccc(-n2cc(C3CC3)nn2)cc1'
>>
>>
>> Notice that I added the bioisostere itself to the products of the
>> reaction as SMILES. You don't want query features there.
>>
>> I hope this helps,
>> -greg
>>
>>
>>
>>
>> On Mon, Feb 5, 2018 at 10:07 AM, Alexis Parenty <
>> alexis.parenty.h...@gmail.com> wrote:
>>
>>> Dear RDKiters,
>>>
>>> I would like to generate the bioisosters of amides from a large list of
>>> structures:
>>>
>>> The smarts patterns for the bioisosters  of amides I am interested in is:
>>>
>>> smarts_path = ['C1=CN=[CH1][CH1]=N1', 'C1=[CH1]N=C[CH1]=N1',
>>> 'C1=[CH1]N=[CH1]C=N1', 'OC1=[CH1]C=NO1', 'OC1=NOC=[CH1]1',
>>> 'C1=CN=C([NX3])O1', '[#6X4]([#6X4](F)(F)(F))[NX3]', 'C(C#N)=NO',
>>> 'N1N=NN=C1', 'N1N=NC=[N]1', 'N1N=NC=[CH1]1', 'C1=NOC=N1', 'C1=NN=C[OX2]1',
>>> 'C1=NN=C[NH1]1', '[C]1(COC1)[OX2]', '[C]1(COC1)[NX3]',
>>> 'C([NX3H1])=N[CX4H3]', '[CX4]1([CX4][CX4]1)[NX3]',
>>> '[#16X4+2]([NX3])([OX1-])([OX1-])', '[#16X4]([NX3])(=[OX1])(=[OX1])',
>>> '[CX3](=[CX3])(F)', '[OX2][CX3](=[OX1])', '[NX3][CX3](=[OX1])']
>>>
>>> How would you best "disconnect the amide moiety" of a structure and
>>> "replace" it with the recursive smarts pattern of its bioisosters? The
>>> bioster matching patern above must be contained within a single smarts, so
>>> I think I need recursive smarts, right?
>>>
>>> Any directions would be very much appreciated.
>>>
>>> Best,
>>>
>>> Alexis
>>>
>>>
>>>
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>>
>
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